Life from Scratch, Almost

Over recent decades there have been many advances in our understanding of genomes. The sequencing of whole genomes was of particular importance. The first full sequence was achieved in 1977 of a phage virus followed 18 years later by the first bacterium, Haemophilus influenzae. Thousands of whole microbial genomes now exist and has enabled advances in techniques like metagenomics and biotechnology.

Perhaps the most controversial study was carried out by Gibson et al (2010) where the creation of an artificial bacterium had been achieved. It got a lot of coverage in the news and as well as a lot of criticism, ‘playing God’ was a term used a lot. This team managed to insert a 1.08 Mbp man made genome into a Mycoplasma capricolum recipient cell. This article does not have the conventional layout but is basically a large Methods section explaining how the cell was produced.

To start with, the artificial genome was based on another species of Mycoplasma (M. mycoides). As this was very experimental procedure these two species were used because of their relatively small genomes. Synthetic genome assembly was done in a number of stages. First step involved a computer and an oligonucleotide synthesizer to produce small DNA segments, 109 of these were joined together to produce 1080-bp long sections. It was very important that these were in the correct sequence in accordance with the M. mycoides genome and this was constantly checked. The following steps involved the gradual build up of the full genome from smaller sections in yeast cells (Saccharomyces cerevisiae). The final chromosome was pieced together from 11 100-kb fragments. The final step was to transplant the entire genome from the yeast to the M. capricolum cells. It was important to switch off any restriction enzymes before hand as they could cleave any foreign DNA. During synthesis of the genome, a number of ‘watermark’ genes were additionally added to confirm that the cells contained the new synthetic genome. One of these watermarks was for proteins that convert X-gal (in the agar plates) into a blue compound. Wild type M. capricolum lack these genes which helped to isolate cells that contained the cloned DNA. The cells were found to be self-sustaining and replicate.

Although this is not strictly marine microbiology, I chose to review it because one of the researchers involved with the project was J. Craig Venter who has become famous for his work on the Global Ocean Survey where thousands of microbial genes are being identified with his whole genome shotgun sequencing technique. With an entire manmade genome having been successfully inserted into a cell it seems certain that highly specialised cells can be made to order for biotechnology. No doubt some of the genes J. Craig Venter has identified will become a major player in producing products like biofuels and pharmaceuticals.

I have only given a very, very brief over view of the technique used in this study, mainly because it is fairly complex but very interesting all the same. The controversy behind it also add an interesting angle to it, if not slightly amusing.

A Review of:
Gibson D, Glass J, Lartigue C, Noskov V, Chuang R, Algire M, Benders G, Montague M, Ma L, Moodie M, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova E, Young L, Qi Z, Segall-Shapiro T, Calvey C, Parmar P, Hutchison C, Smith H and Venter J (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science. 329: 52-58.